Inhomogeneous etching of nanocrystalline diamond (NCD) films, which produces nanopillars during reactive ion etching process, is problematic to the microfabrication of NCD films for the sensor and actuator applications. Thus, its origin was investigated for various initial microstructures of the NCD films, SF6/O2 gas ratios during etching, and plasma powers. The etched NCD film surface roughness became more pronounced (leading to larger pillar diameters and heights) for larger initial microstructural features (larger grain and cluster sizes), particularly at low plasma powers. The surface roughening was significantly reduced with the addition of SF6, almost disappearing at SF6/O2 of 5% to 10%. These results indicate that the etch rate was locally enhanced at the interfaces between grains or clusters, and the etch rate disparity between intragranular and intergranular (or cluster) carbons increased with decreasing ion energy, implying a chemical reaction rate-limited etching mechanism. The role of SF6 could be explained to reduce the energy barrier for the chemical reaction of intragranular carbons. Here we suggest that the etching rate is limited by an energy barrier that could be reduced by defect generation during ion bombardment or by catalytic radicals.